Alina Chan Profile picture
Sep 25, 2020 17 tweets 9 min read Read on X
There's some confusion about how new the D614G mutation is. I'm going to use data on @GISAID visualized by @CovidCg to answer this question. The first time it appeared in China was Jan 23, 2020. So this mutation occurred pretty early on in the outbreak before travel restrictions.
When+where did D614G first get detected in Europe? It's not possible to tell using GISAID alone because many countries did not sequence virus isolates and deposit data till later in the pandemic. However, you can see that there are EU countries with D614G even in Jan.
It was only after January that travel restrictions started being sporadically imposed on China by other countries but it was too late because SARS2 (including D614G variants), as we now know, was already widespread. thinkglobalhealth.org/article/travel…
Had to remove the UK from the "Compare Locations" analysis in Europe because of how many sequences they've uploaded - just a tsunami that washes out the sequences from other countries. The G614 variants, in blue, are among the earliest sequences found in the UK, including in Jan.
Other European countries saw similar trends as well - D614G was among their earliest sequenced virus isolates and quickly became the more prevalent mutation at that point in the Spike. E.g., Germany shown here, G614 in blue, D614 in grey
Netherlands, G614 variants shown in blue, D614 in grey. Both present in the country since the beginning of the detected outbreak there.
What about countries that were able to curb the spread of COVID? Was it that they were dealt an easier hand of less transmissible SARS2? This is Singapore, D614G mutation was also detected in February, similar time as several European countries. Strangely, D614G did not dominate.
Visit covidcg.org to play around with the data yourself :) This is Taiwan, another country with exceedingly few COVID cases. They detected D614G as early as March but half a year later their country still hasn't exploded with COVID.
South Korea also saw the D614G mutation in March. In both the "Compare SNVs" (left) and "Compare Lineages" (right) mode, you can see how there were distinct waves of the virus in their country.
Japan also saw D614G early - at the end of January. It's by no means a new mutant of SARS2 for many countries. covidcg.org
Even across Africa, D614G has been around since the beginning. Worth pointing out again that it is not just 1 variant or strain of SARS2 that carries D614G. Many distinct SARS2 variants carry the same G614 mutation on top of several other mutations.
One particularly interesting country is Australia. At first glance it looks like D614G (blue) is dominating again. But turns out the new wave is marked more specifically by an S477N (pink) spike mutation. D614G+S477N were detected in Australia in late Jan. covidcg.org
New Zealand, another country that's done a phenomenal job limiting the spread of COVID. D614G has also been there since the beginning. The country was able to bring the new daily cases of COVID down to mostly single digits by late April.
How about states in the US? State name at top left corner of each picture. G614 in blue; D614 in grey.
US states started seeing D614G by early March. This was after China travel restrictions had been implemented early Feb, but EU travel (conferences!) was still ongoing. The Mar announcement of restrictions caused Americans to stampede back from EU (where D614G was rampant) to US.
“We closed the front door with the China travel ban,” New York Gov. Andrew M. Cuomo (D) said last month as officials began to grasp the magnitude of the failure. In waiting to cut off travel from Europe, he said, “we left the back door wide open.” washingtonpost.com/world/national…
For more ways to use our free and awesome resource @covidcg covidcg.org please check out our new preprint: biorxiv.org/content/10.110… enabled by @gisaid data contributed by hundreds of different labs around the world.

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More from @Ayjchan

May 14
The soft corruption behind the Proximal Origin letter must be investigated and the authors and their handlers held accountable.

How else will you deter scientists from hiding the involvement of powerful funders in their papers and their "scientific" conclusions?
Jeremy Farrar, the scientist who orchestrated the Proximal Origin letter was not named as an author or acknowledged. He was the director of the Wellcome Trust and had funded one of the authors.

Farrar is now @WHO chief scientist.
@WHO None of these major funders who funded the Proximal Origin authors were acknowledged in the paper although Kristian Andersen privately thanked them for their advice and leadership as they worked on the letter.
Read 7 tweets
May 7
The executive order signed on Monday was not a ban or moratorium on risky pathogen research with the potential to cause pandemics.

It was a charge for OSTP and other agency heads to come up with a new policy & strategy for governing and tracking such research in under 180 days.
I do not see any wording in the executive order asking scientists to pause their research if it falls under the definition of dangerous gain-of-function.
whitehouse.gov/presidential-a…
The executive order is a step in the right direction and I hope that @WHOSTP47 will come up with an improved policy and strategy for pathogen research with catastrophic risks.

But right now, the executive order is not a ban or even a moratorium.
Read 8 tweets
Apr 10
Regarding the possibility that Covid may have spread at the Oct 2019 Wuhan military games, my main question is why noone across multiple countries had the presence of mind to collect & store samples from patients till tests were available.

There should be changes going forward.
According to Under Secretary of Defense for Personnel and Readiness: "Service members were not tested... as testing was not available at this early stage of the pandemic."
freebeacon.com/wp-content/upl…
"athletes noticed that something was amiss in the city of Wuhan.. described it as a “ghost town.”"

"athletes from several countries.. claimed publicly they had contracted what they believed to be covid.. based on their symptoms and how their illnesses spread to their loved ones"
washingtonpost.com/opinions/2021/…
Read 13 tweets
Mar 13
I encourage experts who have insisted on a natural origin of Covid-19 to gracefully change their public stance instead of doubling down on the threadbare evidence for the wet market hypothesis.

You could acknowledge that you initially trusted your colleagues in China/US to tell the truth. But time and time again over the past 5 years, it has been shown that they withheld critical evidence from you and the public:
1⃣The 2018 Defuse proposal
2⃣Low biosafety standards for experiments where live viruses are produced and used in human cell infection studies
3⃣Risky pathogen experiments and surprising gain of function
4⃣Missing pathogen sample database, viruses discovered after 2015 largely not shared with US collaborators
5⃣Closest virus relative that we know of was collected from a mine where people died from suspected SARS-like virus infection

The studies published last month where Wuhan scientists experimented with potentially dangerous pathogens at low biosafety opened your eyes to the level of reckless ambition in their research.

Given these betrayals, it is fully within reason to retract your trust and re-evaluate all the available evidence. Those of you who have access to intelligence could say that the non-public evidence has cast a new light on the public evidence and strengthens the case for a lab origin of Covid-19.

This is better than continuing to argue that you somehow know all the viruses in the Wuhan lab's collection and somehow know they didn't follow through on their 2018 plans to put furin cleavage sites into SARS-like viruses and study these at low biosafety exactly like they said they would.
For those experts who haven't even looked at the Defuse proposal and its drafts, the Wuhan-US scientists clearly said they were interested in furin cleavage sites at the spike S1/S2 junction, and would insert these into novel SARS-like viruses in the lab (not closely related to the 2003 SARS virus as that would be dangerous). They would test the ability of these SARS-like viruses with inserted cleavage sites to infect human cells and cause pathogenesis in vivo.

The Wuhan lab was regularly synthesizing novel coronavirus genomes without leaving any sign of lab manipulation. They used a protocol with trypsin-supplemented media to retain cleavage sites in the viruses. They did much of the work, including infection experiments in human cells, at BSL-2. Their US collaborator Ralph Baric has repeatedly criticized them for doing the work at low biosafety.

h/t @emilyakopp for FOIA'ing the Defuse proposal drafts.Image
Image
Some virologists may argue that the furin cleavage site in SARS-CoV-2 doesn't look canonical. You should read the citation in the Defuse draft for the computational model used to predict furin cleavage sites. The paper says it doesn't rely on the canonical motif and instead looks at a 20-residue sequence to make its predictions. The PRRAR motif exists in a feline coronavirus, MERS has a PRXXR S1/S2 furin cleavage site, and the RRXR motif is a functional furin cleavage site in numerous other proteins.
Read 13 tweets
Mar 12
According to Zeit Online, German Chancellery consulted with US Director of National Intelligence in 2023, who said there was nothing to the lab leak hypothesis.

They doubted "Eierköpfe" (egghead) scientists in intelligence knew better than leading virologists around the world.
In the US, something similar was happening where scientists in intelligence agencies also assessed a likely lab origin of Covid but were sidelined.

"The dominant view within the intelligence community was clear when... the director of national intelligence, and a couple of her senior analysts, briefed Biden... concluded with “low confidence” that Covid-19 had emerged when the virus leapt from an animal to a human."
wsj.com/politics/natio…
In both cases, government leaders favored the opinions of leading virologists over the scientists working in intelligence. Even though some of the leading virologists were public advocates and funders of "gain-of-function" research of concern with pathogens.
Read 4 tweets
Mar 12
German intelligence now assesses a 80-95% likelihood of a lab origin of Covid-19. Image
Image
Read 4 tweets

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